Formal modeling and quantitative analysis of KLAIM-based mobile systems
Proceedings of the 2005 ACM symposium on Applied computing
On codeword design in metric DNA spaces
Natural Computing: an international journal
DNA13'07 Proceedings of the 13th international conference on DNA computing
Towards evolutionary DNA computing
IWINAC'05 Proceedings of the First international conference on Mechanisms, Symbols, and Models Underlying Cognition: interplay between natural and artificial computation - Volume Part I
Designing nucleotide sequences for computation: a survey of constraints
DNA'05 Proceedings of the 11th international conference on DNA Computing
A Molecular Solution to the Three-Partition Problem
Journal of Information Technology Research
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The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequenceCompiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.